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Genomics. 2017 Jul;109(3-4):141-146. doi: 10.1016/j.ygeno.2017.02.002. Epub 2017 Feb 10.

Genome inside genome: NGS based identification and assembly of endophytic Sphingopyxis granuli and Pseudomonas aeruginosa genomes from rice genomic reads.

Author information

1
Centre for Plant Molecular Biology, Osmania University, Hyderabad 500007, Telangana, India.
2
Centre for Plant Molecular Biology, Osmania University, Hyderabad 500007, Telangana, India. Electronic address: kulaganathan123@gmail.com.

Abstract

The interactions between crop plants and the endophytic bacteria colonizing them are poorly understood and experimental methods were found to be inadequate to meet the complexities associated with the interaction. Moreover, research on endophytic bacteria was focused at host plant species level and not at cultivar level which is essential for understanding the role played by them on the productivity of specific crop genotype. High throughput genomics offers valuable tools for identification, characterization of endophytic bacteria and understand their interaction with host plants. In this paper we report the use of high throughput plant genomic data for identification of endophytic bacteria colonizing rice plants. Using this novel next generation sequencing based computational method Sphingopyxis granuli and Pseudomonas aeruginosa were identified as endophytes colonizing the elite indica rice cultivar RP Bio-226 and their draft genome sequences were assembled.

KEYWORDS:

Endophytic bacteria; Genome sequencing; Oryza sativa; Pseudomonas aeruginosa; RP Bio-226; Sphingopyxis granuli

PMID:
28192179
DOI:
10.1016/j.ygeno.2017.02.002
[Indexed for MEDLINE]
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